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comparison masscomb_dbsearch_converter.xml @ 0:d6001e8d7441

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author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 11:34:51 +0100
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1 <tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1">
2 <description> Convert search results to MzIdentML (aka mzid) format</description>
3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 //////////////////////////
7 -->
8 <command interpreter="java -jar">
9 MassComb.jar
10 -action DBSEARCHCONVERT
11 -fileGrouping $fileType.type
12 -searchResultsFormat $fileType.inputFormatType.inputFormat
13 #if $fileType.inputFormatType.inputFormat == "xtandem"
14 -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero
15 #end if
16 -inputFile $fileType.inputFormatType.inputFile
17 -outputFile $outputFile
18 </command>
19 <inputs>
20 <conditional name="fileType">
21 <param name="type" type="select" label="select file grouping type">
22 <option value="single" selected="true">single-File</option>
23 <option value="fileSet">fileSet</option>
24 </param>
25 <when value="single">
26 <conditional name="inputFormatType">
27 <param name="inputFormat" type="select" label="inputFormat">
28 <option value="xtandem">X!Tandem</option>
29 <option value="omssa">OMSSA</option>
30 </param>
31 <when value="xtandem">
32 <param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/>
33 <param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. ">
34 <option value="true" selected="true">Yes, starting at 0</option>
35 <option value="false">No, starting at 1</option>
36 </param>
37 </when>
38 <when value="omssa">
39 <param name="inputFile" type="data" format="omx" label="MS/MS search results"/>
40 </when>
41 </conditional>
42 </when>
43 <when value="fileSet">
44 <conditional name="inputFormatType">
45 <param name="inputFormat" type="select" label="inputFormat">
46 <option value="xtandem">X!Tandem</option>
47 <option value="omssa">OMSSA</option>
48 </param>
49 <when value="xtandem">
50 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results" />
51 <param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. ">
52 <option value="true" selected="true">Yes, starting at 0</option>
53 <option value="false">No, starting at 1</option>
54 </param>
55 </when>
56 <when value="omssa">
57 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/>
58 </when>
59 </conditional>
60 </when>
61 </conditional>
62 </inputs>
63 <outputs>
64 <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} ">
65 <change_format>
66 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/>
67 </change_format>
68 </data>
69 </outputs>
70 <tests>
71 </tests>
72 <help>
73
74 .. class:: infomark
75
76 This tool translates X!Tandem and OMSSA results to mzIdentML format.
77 It uses the library at http://code.google.com/p/mzidentml-parsers/
78 -----
79
80
81 </help>
82 </tool>